It looks like Apple may be doing this for the new 13" rMBP.Brick and mortar stores have an ultimate build which is every BTO option maxed out. I believe they only do this with the MBA (i7/8GB/512SSD 11/13) and the 15" rMBP (fastest i7/16GB/1TSSD). The 13" rMBP doesn't get a true ultimate build at the brick and mortar, they only carry the 3 versions you see on the online store. This is the case for the iMacs as well, very limited options and I think SSD is online only (iMac).
I want into an Apple Store today to buy the high-end stock model. I said, "give me the high-end model." They started to ring up the 13" 3.1 i7/16/? model for about $500 extra before I clarified what I wanted.